Abstract
Our understanding of the causative agents of fungal diseases has changed considerably in recent years due to molecular studies that compare DNA across a wide range of fungi, including human and animal pathogens. In many cases, what had once been understood as traditional species were found to be species complexes. Importantly, members of such complexes may differ in pathogenicity and susceptibility to antifungals, which suggests a need for accurate identification to provide optimal patient care. This article presents a few striking examples from Zygomycetes, Ascomycetes, and Basidiomycetes.
Similar content being viewed by others
References and Recommended Reading
James TY, Kauff F, Schoch CL, et al.: Reconstructing the early evolution of fungi using a six-gene phylogeny. Nature 2006, 443:818–822.
Hibbett DS, Binder M, Bischoff JF, et al.: A higher-level phylogenetic classification of the fungi. Mycol Res 2007, 111:509–547.
Roden MM, Zaoutis TE, Buchanan WL, et al.: Epidemiology and outcome of zygomycosis: a review of 929 reported cases. Clin Infect Dis 2005, 41:634–653.
Zheng RY, Chen GQ, Huang H, Liu XY: A monograph of Rhizopus. Sydowia 2007, 59:273–372.
Hoffmann K, Discher S, Voigt K: Revision of the genus Absidia (Mucorales, Zygomycetes) based on physiological, phylogenetic, and morphological characters; thermotolerant Absidia spp form a coherent group, Mycocladiaceae fam. nov. Mycol Res 2007, 111:1169–1183.
Hoffmann K, Walther G, Voigt K: Mycocladus vs. Lichtheimia: a correction (Lichtheimiaceae fam. nov., Mucorales, Mucoromycotina). Mycol Res 2009, 542:3–4.
Garcia-Hermoso D, Hoinard D, Gantier J-C, et al.: Description of Mycocladus lutetiensis sp. nov., a cryptic species of Mycocladus corymbifer (ex. Absidia corymbifera) associated with human zygomycosis. J Clin Microbiol 2009, In press.
Balajee SA, Borman AM, Brandt ME, et al.: Sequence-based identification of Aspergillus, Fusarium and Mucorales in the clinical mycology laboratory: where are we and where should we go from here? J Clin Microbiol 2009, 47:877–884.
O’Gorman CM, Fuller HT, Dyer PS: Discovery of a sexual cycle in the opportunistic fungal pathogen Aspergillus fumigatus. Nature 2009, 457:471–474.
Alcazar-Fuoli L, Mellado E, Alastruey-Izquierdo A, et al.: Aspergillus section Fumigati: antifungal susceptibility patterns and sequence-based identification. Antimicrob Agents Chemother 2008, 52:1244–1251.
Varga J, Houbraken J, van der Lee HA, et al.: Aspergillus calidoustus sp. nov., causative agent of human infections previously assigned to Aspergillus ustus. Eukaryot Cell 2008, 7:630–638.
Verweij PE, Varga J, Houbraken J, et al.: Emericella quadrilineata as cause of invasive aspergillosis. Emerg Infect Dis 2008, 14:566–572.
Walsh TJ, Petraitis V, Petraitiene R, et al.: Experimental pulmonary aspergillosis due to Aspergillus terreus: pathogenesis and treatment of an emerging fungal pathogen resistant to amphotericin B. J Infect Dis 2003, 188:305–319.
Anaissie EJ, Kuchar RT, Rex JH, et al.: Fusariosis associated with pathogenic fusarium species colonization of a hospital water system: a new paradigm for the epidemiology of opportunistic mold infections. Clin Infect Dis 2001, 33:1871–1878.
O’Donnell K, Sutton DA, Rinaldi MG, et al.: Genetic diversity of human pathogenic members of the Fusarium oxysporum complex inferred from multilocus DNA sequence data and amplified fragment length polymorphism analyses: evidence for the recent dispersion of a geographically widespread clonal lineage and nosocomial origin. J Clin Microbiol 2004, 42:5109–5120.
O’Donnell K, Sarver BAJ, Brandt M, et al.: Phylogenetic diversity and microsphere array-based genotyping of human pathogenic Fusaria, including isolates from the multistate contact lens-associated U.S. keratitis outbreaks of 2005 and 2006. J Clin Microbiol 2007, 45:2235–2248.
O’Donnell K, Sutton DA, Fothergill A, et al.: Molecular phylogenetic diversity, multilocus haplotype nomenclature, and in vitro antifungal resistance within the Fusarium solani species complex. J Clin Microbiol 2008, 46:2477–2490.
Chang DC, Grant GB, O’Donnell K, et al.: Multistate outbreak of Fusarium keratitis associated with use of a contact lens solution. JAMA 2006, 296:953–963.
Summerbell RC, Schroers HJ: Analysis of phylogenetic relationship of Cylindrocarpon lichenicola and Acremonium falciforme to the Fusarium solani species complex and a review of similarities in the spectrum of opportunistic infections caused by these fungi. J Clin Microbiol 2002, 40:2866–2875.
Geiser DM, Jiménez-Gasco MM, Kang S, et al.: FUSARIUMID v. 1.0: a DNA sequence database for identifying Fusarium. Eur J Plant Pathol 2004, 110:473–479.
Queiroz-Telles F, Esterre P, Perez-Blanco M, et al.: Chromoblastomycosis: an overview of clinical manifestations, diagnosis and treatment. Med Mycol 2009, 47:3–15.
Horré R, de Hoog GS: Primary cerebral infections by melanized fungi: a review. Stud Mycol 1991, 43:176–193.
Zeng JS, de Hoog GS: Exophiala spinifera and its allies: diagnostics from morphology to DNA barcoding. Med Mycol 2007, 46:193–208.
Li DM, Ruo YL, de Hoog GS, et al.: Exophiala asiatica, a new species from a fatal case in China. Med Mycol 2009, 47:101–109.
Badali H, Carvalho VO, Vicente V, et al.: Cladophialophora saturnica sp. nov., a new opportunistic species of Chaetothyriales revealed using molecular data. Med Mycol 2009, 47:51–62.
Badali H, Gueidan C, Najafzadeh MJ, et al.: Ecological, morphological and molecular diversity of Cladophialophora. Stud Mycol 2008, 61:175–191.
Najafzadeh M J, Gueidan C, Badali H, et al.: Genetic diversity and species delimitation in the opportunistic genus Fonsecaea. Med Mycol 2009, 47:17–25.
Mostert L, Groenewald JZ, Summerbell RC, et al.: Species of Phaeoacremonium associated with infections in humans and environmental reservoirs in infected woody plants. J Clin Microbiol 2005, 43:1752–1767.
Gilgado F, Cano J, Gené J, et al.: Molecular and phenotypic data supporting distinct species statuses for Scedosporium apiospermum and Pseudallescheria boydii and the proposed new species Scedosporium dehoogii. J Clin Microbiol 2008, 46:766–771.
Kaltseis J, Rainer J, de Hoog GS: Ecological study of Pseudallescheria and Scedosporium species in natural and human-dominated environments. Med Mycol 2009, In press.
Sullivan DJ, Moran GP, Pinjon E, et al.: Comparison of the epidemiology, drug resistance mechanisms, and virulence of Candida dubliniensis and Candida albicans. FEMS Yeast Res 2004, 4:369–376.
Alcoba-Flórez J, Méndez-Alvarez S, Cano J, et al.: Phenotypic and molecular characterization of Candida nivariensis sp. nov., a possible new opportunistic fungus. J Clin Microbiol 2005, 43:4107–4111.
Correia A, Sampaio P, James S, Pais C: Candida bracarensis sp. nov., a novel anamorphic yeast species phenotypically similar to Candida glabrata. Int J Syst Evol Microbiol 2006, 56:313–317.
Lockhart SR, Messer SA, Gherna M, et al.: Identification of Candida nivariensis and Candida bracarensis in a large global collection of Candida glabrata isolates: comparison to the literature. J Clin Microbiol 2009, 47:1216–1217.
Borman AM, Petch R, Linton CJ, et al.: Candida nivariensis, an emerging pathogenic fungus with multidrug resistance to antifungal agents. J Clin Microbiol 2008, 46:933–938.
Bishop JA, Chase N, Magill SS, et al.: Candida bracarensis detected among isolates of Candida glabrata by peptide nucleic acid fluorescence in situ hybridization: susceptibility data and documentation of presumed infection. J Clin Microbiol 2008, 46:443–446.
Tavanti A, Davidson AD, Gow NA, et al.: Candida orthopsilosis and Candida metapsilosis spp nov. to replace Candida parapsilosis groups II and III. J Clin Microbiol 2005, 43:294–292.
Lockhart SR, Messer SA, Pfaller MA, Diekema DJ: Geographic distribution and antifungal susceptibility of the newly described species Candida orthopsilosis and Candida metapsilosis in comparison to the closely related species Candida parapsilosis. J Clin Microbiol 2008, 46:2659–2664.
Odds FC, Jacobsen MD: Multilocus sequence typing of pathogenic Candida species. Eukaryot Cell 2008, 7:1075–1084.
Guého E, Midgley G, Guillot J: The genus Malassezia with description of four new species. Antonie van Leeuwenhoek 1996, 69:337–355.
Batra R, Boekhout T, Guého E, et al.: Malassezia Baillon, emerging clinical yeasts. FEMS Yeast Res 2005, 5:1101–1113.
Xu J, Saunders CW, Hu P, et al.: Dandruff-associated Malassezia genomes reveal convergent and divergent virulence traits shared with plant and human fungal pathogens. Proc Natl Acad Sci U S A 2007, 104:18730–18735.
Bovers M, Hagen F, Kuramae EE, Boekhout T: Six monophyletic lineages identified within Cryptococcus neoformans and Cryptococcus gattii by multi-locus sequence typing. Fungal Genet Biol 2008, 45:400–421.
Viviani MA, Cogliati M, Esposto MC, et al.: Molecular analysis of 311 Cryptococcus neoformans isolates from a 30-month ECMM survey of cryptococcosis in Europe. FEMS Yeast Res 2006, 6:614–619.
Litvintseva AP, Thakur R, Reller LB, Mitchell TG: Prevalence of clinical isolates of Cryptococcus gattii serotype C among patients with AIDS in Sub-Saharan Africa. J Infect Dis 2005, 192:888–892.
Kidd SE, Hagen F, Tscharke RL, et al.: A rare genotype of Cryptococcus gattii caused the cryptococcosis outbreak on Vancouver Island (British Columbia, Canada). Proc Natl Acad Sci USA 2004, 101:17258–17263.
Byrnes III EJ, Bildfell RJ, Frank SA, et al.: Molecular evidence that the range of the Vancouver Island outbreak of Cryptococcus gattii infection has expanded into the Pacific Northwest in the United States. J Infect Dis 2009, 199:1081–1086.
Guého E, Smith MT, de Hoog GS, et al.: Contributions to a revision of the genus Trichosporon. Antonie van Leeuwenhoek 1992, 61:289–316.
Taj-Aldeen SJ, Al-Ansari N, El Shafei S, et al.: Molecular identification and susceptibility of Trichosporon species isolated from clinical specimens in Qatar: isolation of Trichosporon dohaense Taj-Aldeen, Meis & Boekhout sp. nov. J Clin Microbiol 2009 Mar 25 (Epub ahead of print).
Rodriguez-Tudela JL, Diaz-Guerra TM, Mellado E, et al.: Susceptibility patterns and molecular identification of Trichosporon species. Antimicrob Agents Chemother 2005, 49:4026–4034.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Boekhout, T., Gueidan, C., de Hoog, S. et al. Fungal taxonomy: New developments in medically important fungi. Curr Fungal Infect Rep 3, 170–178 (2009). https://doi.org/10.1007/s12281-009-0022-x
Published:
Issue Date:
DOI: https://doi.org/10.1007/s12281-009-0022-x